Procedure for Detecting Outliers in a Circular Regression Model

A number of circular regression models have been proposed in the literature. In recent years, there is a strong interest shown on the subject of outlier detection in circular regression. An outlier detection procedure can be developed by defining a new statistic in terms of the circular residuals. In this paper, we propose a new measure which transforms the circular residuals into linear measures using a trigonometric function. We then employ the row deletion approach to identify observations that affect the measure the most, a candidate of outlier. The corresponding cut-off points and the performance of the detection procedure when applied on Down and Mardia’s model are studied via simulations. For illustration, we apply the procedure on circadian data.     

A Common Fluence Threshold for First Positive and Second Positive Phototropism in Arabidopsis thaliana

The relationship between the amount of light and the amount of response for any photobiological process can be based on the number of incident quanta per unit time (fluence rate-response) or on the number of incident quanta during a given period of irradiation (fluence-response). Fluence-response and fluence rate-response relationships have been measured for second positive phototropism by seedlings of Arabidopsis thaliana. The fluence-response relationships exhibit a single limiting threshold at about 0.01 micromole per square meter when measured at fluence rates from 2.4 × 10⁻⁵ to 6.5 × 10⁻³ micromoles per square meter per second. The threshold values in the fluence rateresponse curves decrease with increasing time of irradiation, but show a common fluence threshold at about 0.01 micromole per square meter. These thresholds are the same as the threshold of about 0.01 micromole per square meter measured for first positive phototropism. Based on these data, it is suggested that second positive curvature has a threshold in time of about 10 minutes. Moreover, if the times of irradiation exceed the time threshold, there is a single limiting fluence threshold at about 0.01 micromole per square meter. Thus, the limiting fluence threshold for second positive phototropism is the same as the fluence threshold for first positive phototropism. Based on these data, we suggest that this common fluence threshold for first positive and second positive phototropism is set by a single photoreceptor pigment system.     

Ste18p Is a Positive Control Element in the Mating Process of Candida albicans

Heterotrimeric G proteins are an important class of eukaryotic signaling molecules that have been identified as central elements in the pheromone response pathways of many fungi. In the fungal pathogen Candida albicans, the STE18 gene (ORF19.6551.1) encodes a potential γ subunit of a heterotrimeric G protein; this protein contains the C-terminal CAAX box characteristic of γ subunits and has sequence similarity to γ subunits implicated in the mating pathways of a variety of fungi. Disruption of this gene was shown to cause sterility of MTLa mating cells and to block pheromone-induced gene expression and shmoo formation; deletion of just the CAAX box residues is sufficient to inactivate Ste18 function in the mating process. Intriguingly, ectopic expression behind the strong ACT1 promoter of either the Gα or the Gβ subunit of the heterotrimeric G protein is able to suppress the mating defect caused by deletion of the Gγ subunit and restore both pheromone-induced gene expression and morphology changes.     

Novel Antimicrobial Peptides That Inhibit Gram Positive Bacterial Exotoxin Synthesis

Gram-positive bacteria, such as Staphylococcus aureus, cause serious human illnesses through combinations of surface virulence factors and secretion of exotoxins. Our prior studies using the protein synthesis inhibitor clindamycin and signal transduction inhibitors glycerol monolaurate and α-globin and β-globin chains of hemoglobin indicate that their abilities to inhibit exotoxin production by S. aureus are separable from abilities to inhibit growth of the organism. Additionally, our previous studies suggest that inhibition of exotoxin production, in absence of ability to kill S. aureus and normal flora lactobacilli, will prevent colonization by pathogenic S. aureus, while not interfering with lactobacilli colonization. These disparate activities may be important in development of novel anti-infective agents that do not alter normal flora. We initiated studies to explore the exotoxin-synthesis-inhibition activity of hemoglobin peptides further to develop potential agents to prevent S. aureus infections. We tested synthesized α-globin chain peptides, synthetic variants of α-globin chain peptides, and two human defensins for ability to inhibit exotoxin production without significantly inhibiting S. aureus growth. All of these peptides were weakly or not inhibitory to bacterial growth. However, the peptides were inhibitory to exotoxin production with increasing activity dependent on increasing numbers of positively-charged amino acids. Additionally, the peptides could be immobilized on agarose beads or have amino acid sequences scrambled and still retain exotoxin-synthesis-inhibition. The peptides are not toxic to human vaginal epithelial cells and do not inhibit growth of normal flora L. crispatus. These peptides may interfere with plasma membrane signal transduction in S. aureus due to their positive charges.     

A Nuclear Factor Recognizing a Positive Regulatory Upstream Element of the Antirrhinum majus Chalcone Synthase Promoter

A positive regulatory element directing maximal expression of the Antirrhinum majus chalcone synthase promoter was characterized by protein-DNA-interaction studies and cis deletion analysis. The positive regulatory element consists of a 47 base pair direct repeat between positions −564 and −670 and provides three binding sites for nuclear protein factors from Nicotiana tabacum and Antirrhinum majus. Oligonucleotide competition assays revealed that the same factor(s) interact(s) with all three binding sites. Transient expression of chimeric chalcone synthase-neomycin phosphotransferase II genes in parsley protoplasts demonstrated that both halves of the 47 base pair repeat element are required for its in vivo function. A possible role of redundant binding sites for the positive regulatory function of the 47 base pair repeat element is discussed.     

Localized, Positive Charge Mediates Adhesion of Rhodosporidium toruloides to Barley Leaves and Polystyrene

The physicochemical forces that mediate attachment of yeasts to the phylloplane are unknown. Cell surface charge and hydrophobicity and adhesion to polystyrene, glass, and barley were assessed for wild-type Rhodosporidium toruloides and attachment-minus (Att⁻) mutants. Cells were grown under conditions promoting (excess carbon) or not promoting (excess nitrogen) capsule production. Hydrophobicity was measured by adhesion to xylenes, and surface charge characteristics were assessed by attachment to either DEAE (positive)- or carboxymethyl (CM) (negative)-Sephadex ion-exchange beads. Hydrophobicity and adhesiveness of nonencapsulated, wild-type R. toruloides decreased from mid-log to late stationary phase. Encapsulated wild-type R. toruloides cells were more hydrophobic and more adhesive than nonencapsulated cells. However, two encapsulated Att⁻ mutants were more hydrophobic than the wild type and levels of adhesion of R. toruloides were similar on polystyrene and less hydrophobic glass surfaces. Adhesion of wild-type yeast to barley and polystyrene was correlated with attachment to CM-Sephadex beads, indicating a positive cell surface charge. Sixteen Att⁻ mutants did not exhibit a positive cell surface charge, and wild-type yeast cells that did not attach to CM-Sephadex did not adhere to either polystyrene or barley. Wild-type R. toruloides attached to CM-Sephadex beads by the poles of the cells, indicating a localization of positive charge which was also visualized with India ink. We conclude that localized, positive charge, and not hydrophobic interactions, mediates attachment of R. toruloides to barley leaves.     

A Hybrid One-Way ANOVA Approach for the Robust and Efficient Estimation of Differential Gene Expression with Multiple Patterns

Background

Identifying genes that are differentially expressed (DE) between two or more conditions with multiple patterns of expression is one of the primary objectives of gene expression data analysis. Several statistical approaches, including one-way analysis of variance (ANOVA), are used to identify DE genes. However, most of these methods provide misleading results for two or more conditions with multiple patterns of expression in the presence of outlying genes. In this paper, an attempt is made to develop a hybrid one-way ANOVA approach that unifies the robustness and efficiency of estimation using the minimum β-divergence method to overcome some problems that arise in the existing robust methods for both small- and large-sample cases with multiple patterns of expression.

Results

The proposed method relies on a β-weight function, which produces values between 0 and 1. The β-weight function with β = 0.2 is used as a measure of outlier detection. It assigns smaller weights (≥ 0) to outlying expressions and larger weights (≤ 1) to typical expressions. The distribution of the β-weights is used to calculate the cut-off point, which is compared to the observed β-weight of an expression to determine whether that gene expression is an outlier. This weight function plays a key role in unifying the robustness and efficiency of estimation in one-way ANOVA.

Conclusion

Analyses of simulated gene expression profiles revealed that all eight methods (ANOVA, SAM, LIMMA, EBarrays, eLNN, KW, robust BetaEB and proposed) perform almost identically for m = 2 conditions in the absence of outliers. However, the robust BetaEB method and the proposed method exhibited considerably better performance than the other six methods in the presence of outliers. In this case, the BetaEB method exhibited slightly better performance than the proposed method for the small-sample cases, but the the proposed method exhibited much better performance than the BetaEB method for both the small- and large-sample cases in the presence of more than 50% outlying genes. The proposed method also exhibited better performance than the other methods for m > 2 conditions with multiple patterns of expression, where the BetaEB was not extended for this condition. Therefore, the proposed approach would be more suitable and reliable on average for the identification of DE genes between two or more conditions with multiple patterns of expression.     

Circular distributions based on nonnegative trigonometric sums

A new family of distributions for circular random variables is proposed. It is based on nonnegative trigonometric sums and can be used to model data sets which present skewness and/or multimodality. In this family of distributions, the trigonometric moments are easily expressed in terms of the parameters of the distribution. The proposed family is applied to two data sets, one related with the directions taken by ants and the other with the directions taken by turtles, to compare their goodness of fit versus common distributions used in the literature.     

On the Relation between Effector Concentration and the Rate of Induced Enzyme Synthesis

The Jacob and Monod scheme for the regulation of enzyme formation leads to the following relation between the relative rate of enzyme synthesis α and cellular effector concentration E (the lower sign is for repressible systems): log (α/1 - α - α_b) = ± n log [E] + log α_b ± log K₁. This equation permits linear plotting of experimental data and the evaluation of three quantities: n, the number of effector molecules combining with a repressor molecule, K₁, the dissociation constant of this interaction and K₂/R_t, the ratio of repressor-operator dissociation constant to total repressor concentration. Measurements on the repression of alkaline phosphatase in Escherichia coli as a function of phosphate concentration are reported and fit the proposed equation with n = 1, indicating that the binding of a single phosphate to the repressor species may be sufficient to cause repression. K₁ of this interaction was found to be 0.58 ±0.11 × 10^-3 M. The available data regarding the enzymes of the lac operon in a variety of E. coli strains, and several other enzymes are analyzed. It is confirmed that the lac repressor interacts with 2 isopropyl thiogalactoside (IPTG) molecules to relieve repression with a K₁ = 50 ±20 × 10^-12 M². In some strains, separate binding constants for the first and second IPTG molecules can be evaluated.     

Mechanosensation in an adipose fin

Adipose fins are found on approximately 20% of ray-finned fish species. The apparently rudimentary anatomy of adipose fins inspired a longstanding hypothesis that these fins are vestigial and lack function. However, adipose fins have evolved repeatedly within Teleostei, suggesting adaptive function. Recently, adipose fins were proposed to function as mechanosensors, detecting fluid flow anterior to the caudal fin. Here we test the hypothesis that adipose fins are mechanosensitive in the catfish Corydoras aeneus. Neural activity, recorded from nerves that innervate the fin, was shown to encode information on both movement and position of the fin membrane, including the magnitude of fin membrane displacement. Thus, the adipose fin of C. aeneus is mechanosensitive and has the capacity to function as a ‘precaudal flow sensor’. These data force re-evaluation of adipose fin clipping, a common strategy for tagging fishes, and inform hypotheses of how function evolves in novel vertebrate appendages.     

From chlorite dismutase towards HemQ–the role of the proximal H-bonding network in haeme binding

Chlorite dismutase (Cld) and HemQ are structurally and phylogenetically closely related haeme enzymes differing fundamentally in their enzymatic properties. Clds are able to convert chlorite into chloride and dioxygen, whereas HemQ is proposed to be involved in the haeme b synthesis of Gram-positive bacteria. A striking difference between these protein families concerns the proximal haeme cavity architecture. The pronounced H-bonding network in Cld, which includes the proximal ligand histidine and fully conserved glutamate and lysine residues, is missing in HemQ. In order to understand the functional consequences of this clearly evident difference, specific hydrogen bonds in Cld from ‘Candidatus Nitrospira defluvii’ (NdCld) were disrupted by mutagenesis. The resulting variants (E210A and K141E) were analysed by a broad set of spectroscopic (UV–vis, EPR and resonance Raman), calorimetric and kinetic methods. It is demonstrated that the haeme cavity architecture in these protein families is very susceptible to modification at the proximal site. The observed consequences of such structural variations include a significant decrease in thermal stability and also affinity between haeme b and the protein, a partial collapse of the distal cavity accompanied by an increased percentage of low-spin state for the E210A variant, lowered enzymatic activity concomitant with higher susceptibility to self-inactivation. The high-spin (HS) ligand fluoride is shown to exhibit a stabilizing effect and partially restore wild-type Cld structure and function. The data are discussed with respect to known structure–function relationships of Clds and the proposed function of HemQ as a coprohaeme decarboxylase in the last step of haeme biosynthesis in Firmicutes and Actinobacteria.     

Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function

Gap penalty is an important component of the scoring scheme that is needed when searching for homologous proteins and for accurate alignment of protein sequences. Most homology search and sequence alignment algorithms employ a heuristic ‘affine gap penalty’ scheme q + r × n, in which q is the penalty for opening a gap, r the penalty for extending it and n the gap length. In order to devise a more rational scoring scheme, we examined the pattern of gaps that occur in a database of structurally aligned protein domain pairs. We find that the logarithm of the frequency of gaps varies linearly with the length of the gap, but with a break at a gap of length 3, and is well approximated by two linear regression lines with R² values of 1.0 and 0.99. The bilinear behavior is retained when gaps are categorized by secondary structures of the two residues flanking the gap. Similar results were obtained when another, totally independent, structurally aligned protein pair database was used. These results suggest a modification of the affine gap penalty function.     

An Improvement of Robust Biometrics-Based Authentication and Key Agreement Scheme for Multi-Server Environments Using Smart Cards

In multi-server environments, user authentication is a very important issue because it provides the authorization that enables users to access their data and services; furthermore, remote user authentication schemes for multi-server environments have solved the problem that has arisen from user’s management of different identities and passwords. For this reason, numerous user authentication schemes that are designed for multi-server environments have been proposed over recent years. In 2015, Lu et al. improved upon Mishra et al.’s scheme, claiming that their remote user authentication scheme is more secure and practical; however, we found that Lu et al.’s scheme is still insecure and incorrect. In this paper, we demonstrate that Lu et al.’s scheme is vulnerable to outsider attack and user impersonation attack, and we propose a new biometrics-based scheme for authentication and key agreement that can be used in multi-server environments; then, we show that our proposed scheme is more secure and supports the required security properties.     

A Positive Feedback Loop Involving Gcm1 and Fzd5 Directs Chorionic Branching Morphogenesis in the Placenta

Chorioallantoic branching morphogenesis is a key milestone during placental development, creating the large surface area for nutrient and gas exchange, and is therefore critical for the success of term pregnancy. Several Wnt pathway molecules have been shown to regulate placental development. However, it remains largely unknown how Wnt-Frizzled (Fzd) signaling spatiotemporally interacts with other essential regulators, ensuring chorionic branching morphogenesis and angiogenesis during placental development. Employing global and trophoblast-specific Fzd5-null and Gcm1-deficient mouse models, combining trophoblast stem cell lines and tetraploid aggregation assay, we demonstrate here that an amplifying signaling loop between Gcm1 and Fzd5 is essential for normal initiation of branching in the chorionic plate. While Gcm1 upregulates Fzd5 specifically at sites where branching initiates in the basal chorion, this elevated Fzd5 expression via nuclear β-catenin signaling in turn maintains expression of Gcm1. Moreover, we show that Fzd5-mediated signaling induces the disassociation of cell junctions for branching initiation via downregulating ZO-1, claudin 4, and claudin 7 expressions in trophoblast cells at the base of the chorion. In addition, Fzd5-mediated signaling is also important for upregulation of Vegf expression in chorion trophoblast cells. Finally, we demonstrate that Fzd5-Gcm1 signaling cascade is operative during human trophoblast differentiation. These data indicate that Gcm1 and Fzd5 function in an evolutionary conserved positive feedback loop that regulates trophoblast differentiation and sites of chorionic branching morphogenesis.     

GEOTROPIC ORIENTATION IN ARTHROPODS : III. THE FIDDLER CRAB UCA.

On an inclined surface the fiddler crab Uca pugnax, during sidewise progression, orients upward through an angle θ on the surface. The extent of negatively geotropic orientation (θ) is a rectilinear function of sin α, where α is the inclination of the surface to the horizontal. This equation differs from that describing the geotropic orientation of various other animals. The difference is traced to the fact that from an initial position with the transverse axis of the body horizontal the crab is required to turn upward to an extent such that the vertical line from its center of gravity pierces the inclined surface within the base of support provided by the legs. This leads to the equation sec θ/tan α = const., which is obeyed within the limits of precision of the measurements. This type of control of geotropic orientation represents an extension of the "muscle tension theory," and is in no sense in conflict with this view. The assumptions underlying the analytical expression connecting θ and α are verified by the asymmetry in the orientation of male fiddlers, which is shown to be due to the presence of the enlarged chela and which disappears when the claws are removed.     

Time Efficient 3D Radial UTE Sampling with Fully Automatic Delay Compensation on a Clinical 3T MR Scanner

This work’s aim was to minimize the acquisition time of a radial 3D ultra-short echo-time (UTE) sequence and to provide fully automated, gradient delay compensated, and therefore artifact free, reconstruction. The radial 3D UTE sequence (echo time 60 μs) was implemented as single echo acquisition with center-out readouts and improved time efficient spoiling on a clinical 3T scanner without hardware modifications. To assess the sequence parameter dependent gradient delays each acquisition contained a quick calibration scan and utilized the phase of the readouts to detect the actual k-space center. This calibration scan does not require any user interaction. To evaluate the robustness of this automatic delay estimation phantom experiments were performed and 19 in vivo imaging data of the head, tibial cortical bone, feet and lung were acquired from 6 volunteers. As clinical application of this fast 3D UTE acquisition single breath-hold lung imaging is demonstrated. The proposed sequence allowed very short repetition times (TR~1ms), thus reducing total acquisition time. The proposed, fully automated k-phase based gradient delay calibration resulted in accurate delay estimations (difference to manually determined optimal delay −0.13 ± 0.45 μs) and allowed unsupervised reconstruction of high quality images for both phantom and in vivo data. The employed fast spoiling scheme efficiently suppressed artifacts caused by incorrectly refocused echoes. The sequence proved to be quite insensitive to motion, flow and susceptibility artifacts and provides oversampling protection against aliasing foldovers in all directions. Due to the short TR, acquisition times are attractive for a wide range of clinical applications. For short T2* mapping this sequence provides free choice of the second TE, usually within less scan time as a comparable dual echo UTE sequence.     

Uncovering the Mechanism of Trapping and Cell Orientation during Neisseria gonorrhoeae Twitching Motility

Neisseria gonorrheae bacteria are the causative agent of the second most common sexually transmitted infection in the world. The bacteria move on a surface by means of twitching motility. Their movement is mediated by multiple long and flexible filaments, called type IV pili, that extend from the cell body, attach to the surface, and retract, thus generating a pulling force. Moving cells also use pili to aggregate and form microcolonies. However, the mechanism by which the pili surrounding the cell body work together to propel bacteria remains unclear. Understanding this process will help describe the motility of N. gonorrheae bacteria, and thus the dissemination of the disease which they cause. In this article we track individual twitching cells and observe that their trajectories consist of alternating moving and pausing intervals, while the cell body is preferably oriented with its wide side toward the direction of motion. Based on these data, we propose a model for the collective pili operation of N. gonorrheae bacteria that explains the experimentally observed behavior. Individual pili function independently but can lead to coordinated motion or pausing via the force balance. The geometry of the cell defines its orientation during motion. We show that by changing pili substrate interactions, the motility pattern can be altered in a predictable way. Although the model proposed is tangibly simple, it still has sufficient robustness to incorporate further advanced pili features and various cell geometries to describe other bacteria that employ pili to move on surfaces.     

Mechanistic Approach to the Problem of Hybridization Efficiency in Fluorescent In Situ Hybridization

In fluorescent in situ hybridization (FISH), the efficiency of hybridization between the DNA probe and the rRNA has been related to the accessibility of the rRNA when ribosome content and cell permeability are not limiting. Published rRNA accessibility maps show that probe brightness is sensitive to the organism being hybridized and the exact location of the target site and, hence, it is highly unpredictable based on accessibility only. In this study, a model of FISH based on the thermodynamics of nucleic acid hybridization was developed. The model provides a mechanistic approach to calculate the affinity of the probe to the target site, which is defined as the overall Gibbs free energy change (ΔG°_overall) for a reaction scheme involving the DNA-rRNA and intramolecular DNA and rRNA interactions that take place during FISH. Probe data sets for the published accessibility maps and experiments targeting localized regions in the 16S rRNA of Escherichia coli were used to demonstrate that ΔG°_overall is a strong predictor of hybridization efficiency and superior to conventional estimates based on the dissociation temperature of the DNA/rRNA duplex. The use of the proposed model also allowed the development of mechanistic approaches to increase probe brightness, even in seemingly inaccessible regions of the 16S rRNA. Finally, a threshold ΔG°_overall of −13.0 kcal/mol was proposed as a goal in the design of FISH probes to maximize hybridization efficiency without compromising specificity.     

High Rates of Homologous Recombination in the Mite Endosymbiont and Opportunistic Human Pathogen Orientia tsutsugamushi

Orientia tsutsugamushi is an intracellular α-proteobacterium which resides in trombiculid mites, and is the causative agent of scrub typhus in East Asia. The genome sequence of this species has revealed an unprecedented number of repeat sequences, most notably of the genes encoding the conjugative properties of a type IV secretion system (T4SS). Although this observation is consistent with frequent intragenomic recombination, the extent of homologous recombination (gene conversion) in this species is unknown. To address this question, and to provide a protocol for the epidemiological surveillance of this important pathogen, we have developed a multilocus sequence typing (MLST) scheme based on 7 housekeeping genes (gpsA, mdh, nrdB, nuoF, ppdK, sucD, sucB). We applied this scheme to the two published genomes, and to DNA extracted from blood taken from 84 Thai scrub typhus patients, from 20 cultured Thai patient isolates, 1 Australian patient sample, and from 3 cultured type strains. These data demonstrated that the O. tsutsugamushi population was both highly diverse [Simpson''s index (95% CI) = 0.95 (0.92–0.98)], and highly recombinogenic. These results are surprising given the intracellular life-style of this species, but are broadly consistent with results obtained for Wolbachia, which is an α-proteobacterial reproductive parasite of arthropods. We also compared the MLST data with ompA sequence data and noted low levels of consistency and much higher discrimination by MLST. Finally, twenty-five percent of patients in this study were simultaneously infected with multiple sequence types, suggesting multiple infection caused by either multiple mite bites, or multiple strains co-existing within individual mites.     

Development and Application of Stereo Camera-Based Upper Extremity Workspace Evaluation in Patients with Neuromuscular Diseases

Background

The concept of reachable workspace is closely tied to upper limb joint range of motion and functional capability. Currently, no practical and cost-effective methods are available in clinical and research settings to provide arm-function evaluation using an individual’s three-dimensional (3D) reachable workspace. A method to intuitively display and effectively analyze reachable workspace would not only complement traditional upper limb functional assessments, but also provide an innovative approach to quantify and monitor upper limb function.

Methodology/Principal Findings

A simple stereo camera-based reachable workspace acquisition system combined with customized 3D workspace analysis algorithm was developed and compared against a sub-millimeter motion capture system. The stereo camera-based system was robust, with minimal loss of data points, and with the average hand trajectory error of about 40 mm, which resulted to ∼5% error of the total arm distance. As a proof-of-concept, a pilot study was undertaken with healthy individuals (n = 20) and a select group of patients with various neuromuscular diseases and varying degrees of shoulder girdle weakness (n = 9). The workspace envelope surface areas generated from the 3D hand trajectory captured by the stereo camera were compared. Normalization of acquired reachable workspace surface areas to the surface area of the unit hemi-sphere allowed comparison between subjects. The healthy group’s relative surface areas were 0.618±0.09 and 0.552±0.092 (right and left), while the surface areas for the individuals with neuromuscular diseases ranged from 0.03 and 0.09 (the most severely affected individual) to 0.62 and 0.50 (very mildly affected individual). Neuromuscular patients with severe arm weakness demonstrated movement largely limited to the ipsilateral lower quadrant of their reachable workspace.

Conclusions/Significance

The findings indicate that the proposed stereo camera-based reachable workspace analysis system is capable of distinguishing individuals with varying degrees of proximal upper limb functional impairments.